Highly flexible protein-peptide docking using CABS-dockMethods in Molecular Biology 1561, 69-94, 2017.
Modeling EphB4-EphrinB2 protein–protein interaction using flexible docking of a short linear motifBioMedical Engineering OnLine, doi: 10.1186/s12938-017-0362-7 , 2017.
Flexible protein-peptide docking using CABS-dock with knowledge about the binding siteProceedings of the International Work-conference on Bioinformatics and BIOmedical engineering (IWWBIO) in Granada, Spain, 195-201, arXiv:1605.09269 , 2016.
Protein-peptide molecular docking with large-scale conformational changes: the p53-MDM2 interactionScientific Reports 6, 37532, 2016.
Towards protein-protein docking with significant structural changes using CABS-dockProceedings of the International Work-conference on Bioinformatics and BIOmedical engineering (IWWBIO) in Granada, Spain, 207-213, arXiv:1605.09266 , 2016.
CABS-dock web server for the flexible docking of peptides to proteins without prior knowledge of the binding siteNucleic Acids Research 43 (W1), W419-W424, 2015.
Coarse-grained modeling of protein structure, dynamics and protein-protein interactionsTASK Quarterly 18, 219–229, 2014.
Flexible docking of the fragment of the troponin I to the troponin CIWBBIO 2014 (2nd International Work-Conference on Bioinformatics and Biomedical Engineering) , 2014.
Analysis and optimization of interactions between peptides mimicking the GD2 ganglioside and the monoclonal antibody 14G2aInternational Journal of Molecular Medicine 28, 47–57, 2011.
Human telomerase model shows the role of the TEN domain in advancing the double helix for the next polymerization stepProceedings of the National Academy of Sciences of the United States of America 108, 9443–8, 2011.
MSITE: a new computational tool for comparison of homological proteins in holo formThe Journal of Steroid Biochemistry and Molecular Biology 121, 34-42, 2010.
Theoretical study of molecular mechanism of binding TRAP220 coactivator to Retinoid X Receptor alpha, activated by 9-cis retinoic acidThe Journal of Steroid Biochemistry and Molecular Biology 121, 124–9, 2010.
Template-free predictions of three-dimensional protein structures: From first principles to knowledge-based potentialsPrediction of Protein Structures, Functions, and Interactions 117-142, 2008.
Steps towards flexible docking: modeling of three-dimensional structures of the nuclear receptors bound with peptide ligands mimicking co-activators' sequencesThe Journal of Steroid Biochemistry and Molecular Biology 103, 357–60, 2007.
Clustering as a supporting tool for structural drug designActa Poloniae Pharmaceutica. Drug Research 63, 436-8, 2006.
Denatured proteins and early folding intermediates simulated in a reduced conformational spaceActa Biochimica Polonica 53, 131–143, 2006.